As Baloo has told you. You will need to include the Medical Exam with the submission of your application for PR status. I recommend getting it done as close to the time you are submitting your application because otherwise if you get it done too early you may be asked to take another one during the process adding extra money to be spent later and adding a few months delay. The medical is valid for 12 months from when you get it done just in case you are wondering. Also make sure you get the medical done in accordance to how you are having it processed. Outland and Inland have different ways of submitting proof of medical so make sure you know which is which.
Also, I can't really recommend a good time to start doing your application because in 2 years time I am sure the process will be completely different and perhaps even more expensive/stricter. They are already looking into the process of changing over the current format to giving probationary visas in this year instead of immediately obtaining PR status. So for now I would just recommend savings up documents to prove the genuineness of your relationship and then when it gets close to 6 months to when you expect to submit it, collect the forms and do more research to make sure you are up to date on the current process at that time then include your documents and send it with lots of luck. For now take your time, enjoy your marriage, and keep collecting evidence until your ready.
